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Mutation (snp-normalizer)
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de.hu.berlin.wbi.objects</FONT>
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Class Mutation</H2>
<PRE>
java.lang.Object
  <IMG SRC="../../../../../resources/inherit.gif" ALT="extended by "><B>de.hu.berlin.wbi.objects.Mutation</B>
</PRE>
<DL>
<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../de/hu/berlin/wbi/psb/object/MutationPSB.html" title="class in de.hu.berlin.wbi.psb.object">MutationPSB</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A></DD>
</DL>
<HR>
<DL>
<DT><PRE>public class <B>Mutation</B><DT>extends java.lang.Object</DL>
</PRE>

<P>
Class to represent a mutation mention found by an NER tool like <a
 href="mutationfinder.sourceforge.net/">MutationFinder</a>.
<P>

<P>
<DL>
<DT><B>Author:</B></DT>
  <DD>philippe</DD>
</DL>
<HR>

<P>

<!-- ======== CONSTRUCTOR SUMMARY ======== -->

<A NAME="constructor_summary"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
<B>Constructor Summary</B></FONT></TH>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#Mutation()">Mutation</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#Mutation(int, de.hu.berlin.wbi.objects.EntityOffset, java.lang.String)">Mutation</A></B>(int&nbsp;pmid,
         <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location,
         java.lang.String&nbsp;mutation)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#Mutation(int, int, de.hu.berlin.wbi.objects.EntityOffset, java.lang.String, java.lang.String[], java.lang.String)">Mutation</A></B>(int&nbsp;pmid,
         int&nbsp;confidence,
         <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location,
         java.lang.String&nbsp;wtResidue,
         java.lang.String[]&nbsp;mutResidues,
         java.lang.String&nbsp;position)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#Mutation(java.lang.String)">Mutation</A></B>(java.lang.String&nbsp;mutation)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Generates a Mutation object from a String like "A123T".</TD>
</TR>
</TABLE>
&nbsp;
<!-- ========== METHOD SUMMARY =========== -->

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<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
<B>Method Summary</B></FONT></TH>
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<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#getConfidence()">getConfidence</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the confidence.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#getLocation()">getLocation</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the location in ??.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;java.lang.String[]</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#getMutResidues()">getMutResidues</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the residues.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#getPmid()">getPmid</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the Pubmed ID.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#getPosition()">getPosition</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the position.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;java.util.List&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt;</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#getPossibledbSNPs(java.util.List)">getPossibledbSNPs</A></B>(java.util.List&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>&gt;&nbsp;candidates)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method evaluates if some of the <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> provided in <b>candidates</b>
 actually equals the text-mined <A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html" title="class in de.hu.berlin.wbi.objects"><CODE>Mutation</CODE></A></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#getWtResidue()">getWtResidue</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the residue.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#isNsm()">isNsm</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if is flag indicating if this SNP is possibly a NSM.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>static&nbsp;java.util.List&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html" title="class in de.hu.berlin.wbi.objects">Mutation</A>&gt;</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#readMutations(java.lang.String)">readMutations</A></B>(java.lang.String&nbsp;file)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method loads Mutations from a file which are in the following format
 described in data/snps.txt (PMID\tWMutM\tstart\tstop)</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#setConfidence(int)">setConfidence</A></B>(int&nbsp;confidence)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the confidence.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#setLocation(de.hu.berlin.wbi.objects.EntityOffset)">setLocation</A></B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the location in ??.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#setMutResidues(java.lang.String[])">setMutResidues</A></B>(java.lang.String[]&nbsp;mutResidues)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the residues.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#setPmid(int)">setPmid</A></B>(int&nbsp;pmid)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the Pubmed ID.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#setPosition(java.lang.String)">setPosition</A></B>(java.lang.String&nbsp;position)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the position.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#setWtResidue(java.lang.String)">setWtResidue</A></B>(java.lang.String&nbsp;wtResidue)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the residue.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#toNormalized()">toNormalized</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html#toString()">toString</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
</TABLE>
&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE>equals, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
</TR>
</TABLE>
&nbsp;
<P>

<!-- ========= CONSTRUCTOR DETAIL ======== -->

<A NAME="constructor_detail"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
<B>Constructor Detail</B></FONT></TH>
</TR>
</TABLE>

<A NAME="Mutation()"><!-- --></A><H3>
Mutation</H3>
<PRE>
public <B>Mutation</B>()</PRE>
<DL>
</DL>
<HR>

<A NAME="Mutation(java.lang.String)"><!-- --></A><H3>
Mutation</H3>
<PRE>
public <B>Mutation</B>(java.lang.String&nbsp;mutation)</PRE>
<DL>
<DD>Generates a Mutation object from a String like "A123T".
<P>
<DL>
<DT><B>Parameters:</B><DD><CODE>mutation</CODE> - </DL>
</DL>
<HR>

<A NAME="Mutation(int, int, de.hu.berlin.wbi.objects.EntityOffset, java.lang.String, java.lang.String[], java.lang.String)"><!-- --></A><H3>
Mutation</H3>
<PRE>
public <B>Mutation</B>(int&nbsp;pmid,
                int&nbsp;confidence,
                <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location,
                java.lang.String&nbsp;wtResidue,
                java.lang.String[]&nbsp;mutResidues,
                java.lang.String&nbsp;position)</PRE>
<DL>
<DL>
<DT><B>Parameters:</B><DD><CODE>pmid</CODE> - <DD><CODE>confidence</CODE> - <DD><CODE>location</CODE> - <DD><CODE>wtResidue</CODE> - <DD><CODE>mutResidues</CODE> - <DD><CODE>position</CODE> - </DL>
</DL>
<HR>

<A NAME="Mutation(int, de.hu.berlin.wbi.objects.EntityOffset, java.lang.String)"><!-- --></A><H3>
Mutation</H3>
<PRE>
public <B>Mutation</B>(int&nbsp;pmid,
                <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location,
                java.lang.String&nbsp;mutation)</PRE>
<DL>
<DL>
<DT><B>Parameters:</B><DD><CODE>pmid</CODE> - <DD><CODE>location</CODE> - <DD><CODE>mutation</CODE> - </DL>
</DL>

<!-- ============ METHOD DETAIL ========== -->

<A NAME="method_detail"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
<B>Method Detail</B></FONT></TH>
</TR>
</TABLE>

<A NAME="getPossibledbSNPs(java.util.List)"><!-- --></A><H3>
getPossibledbSNPs</H3>
<PRE>
public java.util.List&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt; <B>getPossibledbSNPs</B>(java.util.List&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>&gt;&nbsp;candidates)</PRE>
<DL>
<DD>This method evaluates if some of the <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> provided in <b>candidates</b>
 actually equals the text-mined <A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html" title="class in de.hu.berlin.wbi.objects"><CODE>Mutation</CODE></A>
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>candidates</CODE> - List of dbSNP-entries which might actually describe this
            NER-SNP
<DT><B>Returns:</B><DD>normalized mutations</DL>
</DD>
</DL>
<HR>

<A NAME="readMutations(java.lang.String)"><!-- --></A><H3>
readMutations</H3>
<PRE>
public static java.util.List&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/Mutation.html" title="class in de.hu.berlin.wbi.objects">Mutation</A>&gt; <B>readMutations</B>(java.lang.String&nbsp;file)
                                              throws java.io.FileNotFoundException,
                                                     java.io.IOException</PRE>
<DL>
<DD>This method loads Mutations from a file which are in the following format
 described in data/snps.txt (PMID\tWMutM\tstart\tstop)
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>file</CODE> - with mutations
<DT><B>Returns:</B><DD>list of mutations
<DT><B>Throws:</B>
<DD><CODE>java.io.FileNotFoundException</CODE>
<DD><CODE>java.io.IOException</CODE></DL>
</DD>
</DL>
<HR>

<A NAME="getPmid()"><!-- --></A><H3>
getPmid</H3>
<PRE>
public int <B>getPmid</B>()</PRE>
<DL>
<DD>Gets the Pubmed ID.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the Pubmed ID</DL>
</DD>
</DL>
<HR>

<A NAME="setPmid(int)"><!-- --></A><H3>
setPmid</H3>
<PRE>
public void <B>setPmid</B>(int&nbsp;pmid)</PRE>
<DL>
<DD>Sets the Pubmed ID.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>pmid</CODE> - the new Pubmed ID</DL>
</DD>
</DL>
<HR>

<A NAME="getConfidence()"><!-- --></A><H3>
getConfidence</H3>
<PRE>
public int <B>getConfidence</B>()</PRE>
<DL>
<DD>Gets the confidence.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the confidence</DL>
</DD>
</DL>
<HR>

<A NAME="setConfidence(int)"><!-- --></A><H3>
setConfidence</H3>
<PRE>
public void <B>setConfidence</B>(int&nbsp;confidence)</PRE>
<DL>
<DD>Sets the confidence.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>confidence</CODE> - the new confidence</DL>
</DD>
</DL>
<HR>

<A NAME="getLocation()"><!-- --></A><H3>
getLocation</H3>
<PRE>
public <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A> <B>getLocation</B>()</PRE>
<DL>
<DD>Gets the location in ??.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the location in ??</DL>
</DD>
</DL>
<HR>

<A NAME="setLocation(de.hu.berlin.wbi.objects.EntityOffset)"><!-- --></A><H3>
setLocation</H3>
<PRE>
public void <B>setLocation</B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location)</PRE>
<DL>
<DD>Sets the location in ??.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>location</CODE> - the new location in ??</DL>
</DD>
</DL>
<HR>

<A NAME="getWtResidue()"><!-- --></A><H3>
getWtResidue</H3>
<PRE>
public java.lang.String <B>getWtResidue</B>()</PRE>
<DL>
<DD>Gets the residue.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the residue</DL>
</DD>
</DL>
<HR>

<A NAME="setWtResidue(java.lang.String)"><!-- --></A><H3>
setWtResidue</H3>
<PRE>
public void <B>setWtResidue</B>(java.lang.String&nbsp;wtResidue)</PRE>
<DL>
<DD>Sets the residue.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>wtResidue</CODE> - the new residue</DL>
</DD>
</DL>
<HR>

<A NAME="getMutResidues()"><!-- --></A><H3>
getMutResidues</H3>
<PRE>
public java.lang.String[] <B>getMutResidues</B>()</PRE>
<DL>
<DD>Gets the residues.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the residues</DL>
</DD>
</DL>
<HR>

<A NAME="setMutResidues(java.lang.String[])"><!-- --></A><H3>
setMutResidues</H3>
<PRE>
public void <B>setMutResidues</B>(java.lang.String[]&nbsp;mutResidues)</PRE>
<DL>
<DD>Sets the residues.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>mutResidues</CODE> - the new residues</DL>
</DD>
</DL>
<HR>

<A NAME="getPosition()"><!-- --></A><H3>
getPosition</H3>
<PRE>
public java.lang.String <B>getPosition</B>()</PRE>
<DL>
<DD>Gets the position.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the position</DL>
</DD>
</DL>
<HR>

<A NAME="setPosition(java.lang.String)"><!-- --></A><H3>
setPosition</H3>
<PRE>
public void <B>setPosition</B>(java.lang.String&nbsp;position)</PRE>
<DL>
<DD>Sets the position.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>position</CODE> - the new position</DL>
</DD>
</DL>
<HR>

<A NAME="toString()"><!-- --></A><H3>
toString</H3>
<PRE>
public java.lang.String <B>toString</B>()</PRE>
<DL>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>
</DD>
<DD><DL>
</DL>
</DD>
</DL>
<HR>

<A NAME="toNormalized()"><!-- --></A><H3>
toNormalized</H3>
<PRE>
public java.lang.String <B>toNormalized</B>()</PRE>
<DL>
<DD><DL>

<DT><B>Returns:</B><DD>SNP-description following the <wt><aa><mt> nomenclature</DL>
</DD>
</DL>
<HR>

<A NAME="isNsm()"><!-- --></A><H3>
isNsm</H3>
<PRE>
public boolean <B>isNsm</B>()</PRE>
<DL>
<DD>Checks if is flag indicating if this SNP is possibly a NSM.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the flag indicating if this SNP is possibly a NSM</DL>
</DD>
</DL>
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